The MicroArray Explorer or MAExplorer is a Java-based data mining tool for exploring microarray cDNA expression data across multiple microarray hybridizations. Arrays are used to monitor expression profiles under various physiological conditions. MAExplorer is available as either a Web browser applet or a stand-alone application on a user's computer. Stand-alone applications can save and read data on the user's disk for creating custom data mining sessions. It can read data derived from a variety of membrane and glass microarrays, with 33P and Cy3/Cy5 labeling. Other arrays are being added. Database configuration is flexible making it possible to use MAExplorer with other types of arrays. Data may be viewed and directly manipulated in images, scatter plots, histograms, expression profile plots, cluster analysis, etc. Interesting sets of clones may be discovered using a "data filter" that finds a set of clones passing a variety of user-specified tests. Users may generate filtered clone reports which may directly access UniGene, GeneBank, NCI/CIT mAdb and other Internet databases. Report data may be exported to Excel. MAExplorer helps: 1) analyze the expression of individual genes; 2) analyze the expression of gene families and clusters; 3) compare expression patterns for multiple arrays. Data is read from local files on a user's computer or downloaded from a Web array database server. Local array spot quantification files could be obtained directly from an array scanner. Alternatively, when data is downloaded from a Web database server it may be saved (cached) on the user's computer. This avoids long startup times in future data analysis sessions and allows analysis of the data when users are not connected to the Web. The Web site http://www.lecb.ncifcrf.gov/MAExplorer enables users to freely download the stand-alone version of MAExplorer for running on Windows, Macintosh or Unix systems (Sun Solaris, Linux, etc.) as well as providing documentation and tutorials. A Java plugin facility being developed will allow investigators to add their own analysis methods. The MAExplorer (applet version) may be accessed through the Mammary Genome Anatomy Program server at http://mammary.nih.gov/. Z01 BC 10303-01